Dear AMBER users,
I've tried to analyze MD results with clustering. I found manual of ptraj program with following example that produces 5 clusters using a RMS metric comparing the CA atoms:
trajin traj.1.gz
trajin traj.2.gz
cluster out testcluster representative pdb \
average pdb means clusters 5 rms .CA
Now, I won't specify the number of the clusters, but woule like to produce clusters based on the RMSD difference at cutoff = 2 angstrom.
How should I modify the script?
Thanks a lot for the help!
Jack
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Mar 30 2011 - 02:00:03 PDT
